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<div class="title">diffusion_reaction_particles.h</div>  </div>
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<a href="diffusion__reaction__particles_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/* -------------------------------------------------------------------------*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">*                               SPHinXsys                                   *</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">* --------------------------------------------------------------------------*</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* SPHinXsys (pronunciation: s&#39;finksis) is an acronym from Smoothed Particle *</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* Hydrodynamics for industrial compleX systems. It provides C++ APIs for    *</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* physical accurate simulation and aims to model coupled industrial dynamic *</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* systems including fluid, solid, multi-body dynamics and beyond with SPH   *</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* (smoothed particle hydrodynamics), a meshless computational method using  *</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">* particle discretization.                                                  *</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment">* SPHinXsys is partially funded by German Research Foundation               *</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">* (Deutsche Forschungsgemeinschaft) DFG HU1527/6-1, HU1527/10-1             *</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">* and HU1527/12-1.                                                          *</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">* Portions copyright (c) 2017-2020 Technical University of Munich and       *</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">* the authors&#39; affiliations.                                                *</span></div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">* Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may   *</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">* not use this file except in compliance with the License. You may obtain a *</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">* copy of the License at http://www.apache.org/licenses/LICENSE-2.0.        *</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">*                                                                           *</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment">* --------------------------------------------------------------------------*/</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="preprocessor">#pragma once</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160; </div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="base__particles_8h.html">base_particles.h</a>&quot;</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="base__body_8h.html">base_body.h</a>&quot;</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="base__material_8h.html">base_material.h</a>&quot;</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="preprocessor">#include &quot;diffusion_reaction.h&quot;</span></div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="xml__engine_8h.html">xml_engine.h</a>&quot;</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="solid__particles_8h.html">solid_particles.h</a>&quot;</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160; </div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="keyword">namespace </span><a class="code" href="namespace_s_p_h.html">SPH</a> {</div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160; </div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;    <span class="keyword">template</span>&lt;<span class="keyword">class</span> BaseParticlesType = BaseParticles, <span class="keyword">class</span> BaseMaterialType = BaseMaterial&gt;</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;    <span class="keyword">class </span>DiffusionReactionParticles : <span class="keyword">public</span> BaseParticlesType</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;    {</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;    <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00048"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a4295decbe27c9e07483e11c732103c69">   48</a></span>&#160;        <span class="keywordtype">size_t</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a4295decbe27c9e07483e11c732103c69">number_of_species_</a>;              </div>
<div class="line"><a name="l00049"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a8bf449802715f840b83c056a140dd2e4">   49</a></span>&#160;        <span class="keywordtype">size_t</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a8bf449802715f840b83c056a140dd2e4">number_of_diffusion_species_</a>;    </div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;        std::map&lt;std::string, size_t&gt; species_indexes_map_;</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00052"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#acaa27e9af9574ae0075d53cd110dac1d">   52</a></span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#acaa27e9af9574ae0075d53cd110dac1d">species_n_</a>;   </div>
<div class="line"><a name="l00053"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a09aa053be160e695627643c64d111d96">   53</a></span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a09aa053be160e695627643c64d111d96">diffusion_dt_</a>;</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;        <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles</a>(<a class="code" href="class_s_p_h_1_1_s_p_h_body.html">SPHBody</a>* body, </div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial&lt;BaseParticlesType, BaseMaterialType&gt;</a>* diffusion_reaction_material)</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;            : BaseParticlesType(body, diffusion_reaction_material)</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;        {</div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;            diffusion_reaction_material-&gt;assignDiffusionReactionParticles(<span class="keyword">this</span>);</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;            species_indexes_map_ = diffusion_reaction_material-&gt;SpeciesIndexMap();</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a4295decbe27c9e07483e11c732103c69">number_of_species_</a> = diffusion_reaction_material-&gt;NumberOfSpecies();</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#acaa27e9af9574ae0075d53cd110dac1d">species_n_</a>.resize(<a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a4295decbe27c9e07483e11c732103c69">number_of_species_</a>);</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160; </div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;            std::map&lt;std::string, size_t&gt;::iterator itr;</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;            <span class="keywordflow">for</span> (itr = species_indexes_map_.begin(); itr != species_indexes_map_.end(); ++itr) </div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;            {</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;                <span class="comment">//Register a species. Note that we call a template function from a template class</span></div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;                this-&gt;<span class="keyword">template</span> registerAVariable&lt;indexScalar, Real&gt;(<a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#acaa27e9af9574ae0075d53cd110dac1d">species_n_</a>[itr-&gt;second], itr-&gt;first);</div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;                <span class="comment">//the scalars will be sorted if particle sorting is called</span></div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;                this-&gt;<span class="keyword">template</span> registerASortableVariable&lt;indexScalar, Real&gt;(itr-&gt;first);</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;                <span class="comment">// add species to basic output particle data</span></div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;                this-&gt;<span class="keyword">template</span> addAVariableToWrite&lt;indexScalar, Real&gt;(itr-&gt;first);</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;            }</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160; </div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a8bf449802715f840b83c056a140dd2e4">number_of_diffusion_species_</a> = diffusion_reaction_material-&gt;NumberOfSpeciesDiffusion();</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a09aa053be160e695627643c64d111d96">diffusion_dt_</a>.resize(<a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a8bf449802715f840b83c056a140dd2e4">number_of_diffusion_species_</a>);</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;            <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> m = 0; m &lt; <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a8bf449802715f840b83c056a140dd2e4">number_of_diffusion_species_</a>; ++m)</div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;            {</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;                <span class="comment">//----------------------------------------------------------------------</span></div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;                <span class="comment">//  register reactive change rate terms without giving variable name</span></div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;                <span class="comment">//----------------------------------------------------------------------</span></div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;                std::get&lt;indexScalar&gt;(this-&gt;all_particle_data_).push_back(&amp;<a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a09aa053be160e695627643c64d111d96">diffusion_dt_</a>[m]);</div>
<div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;                <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html#a09aa053be160e695627643c64d111d96">diffusion_dt_</a>[m].resize(this-&gt;real_particles_bound_, Real(0));</div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;            }</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;        };</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles</a>() {};</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160; </div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;        std::map&lt;std::string, size_t&gt; SpeciesIndexMap() { <span class="keywordflow">return</span>  species_indexes_map_; };</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160; </div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;        <span class="keyword">virtual</span> DiffusionReactionParticles&lt;BaseParticlesType, BaseMaterialType&gt;*  </div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;            ThisObjectPtr()<span class="keyword"> override </span>{ <span class="keywordflow">return</span> <span class="keyword">this</span>; };</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;    };</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160; </div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_electro_physiology_particles.html">   98</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_electro_physiology_particles.html">ElectroPhysiologyParticles</a> </div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_particles.html">DiffusionReactionParticles&lt;SolidParticles, Solid&gt;</a></div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    {</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;    <span class="keyword">public</span>:</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;        <a class="code" href="class_s_p_h_1_1_electro_physiology_particles.html">ElectroPhysiologyParticles</a>(<a class="code" href="class_s_p_h_1_1_s_p_h_body.html">SPHBody</a>* body, </div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;            <a class="code" href="class_s_p_h_1_1_diffusion_reaction_material.html">DiffusionReactionMaterial&lt;SolidParticles, Solid&gt;</a>* diffusion_reaction_material);</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_electro_physiology_particles.html">ElectroPhysiologyParticles</a>() {};</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;        <span class="keyword">virtual</span> <a class="code" href="class_s_p_h_1_1_electro_physiology_particles.html">ElectroPhysiologyParticles</a>* ThisObjectPtr()<span class="keyword"> override </span>{ <span class="keywordflow">return</span> <span class="keyword">this</span>; };</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160; </div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;    };</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;}</div>
</div><!-- fragment --></div><!-- contents -->
<div class="ttc" id="aclass_s_p_h_1_1_electro_physiology_particles_html"><div class="ttname"><a href="class_s_p_h_1_1_electro_physiology_particles.html">SPH::ElectroPhysiologyParticles</a></div><div class="ttdoc">A group of particles with electrophysiology particle data.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:98</div></div>
<div class="ttc" id="abase__particles_8h_html"><div class="ttname"><a href="base__particles_8h.html">base_particles.h</a></div><div class="ttdoc">This is the base class of SPH particles. The basic data of the particles is saved in separated large ...</div></div>
<div class="ttc" id="asolid__particles_8h_html"><div class="ttname"><a href="solid__particles_8h.html">solid_particles.h</a></div><div class="ttdoc">This is the derived class of base particles.</div></div>
<div class="ttc" id="abase__material_8h_html"><div class="ttname"><a href="base__material_8h.html">base_material.h</a></div><div class="ttdoc">This is the base classes of all materials. A function in a derived material class returns a value wit...</div></div>
<div class="ttc" id="axml__engine_8h_html"><div class="ttname"><a href="xml__engine_8h.html">xml_engine.h</a></div><div class="ttdoc">XML class for xml input and output, this is GUI of simbody xml parser.</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_particles_html_a4295decbe27c9e07483e11c732103c69"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a4295decbe27c9e07483e11c732103c69">SPH::DiffusionReactionParticles::number_of_species_</a></div><div class="ttdeci">size_t number_of_species_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:48</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_particles_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html">SPH::DiffusionReactionParticles</a></div><div class="ttdoc">A group of particles with diffusion or/and reactions particle data.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:43</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_material_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_material.html">SPH::DiffusionReactionMaterial</a></div><div class="ttdoc">Complex material for diffusion or/and reactions.</div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:222</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_particles_html_acaa27e9af9574ae0075d53cd110dac1d"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#acaa27e9af9574ae0075d53cd110dac1d">SPH::DiffusionReactionParticles::species_n_</a></div><div class="ttdeci">StdVec&lt; StdLargeVec&lt; Real &gt; &gt; species_n_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:52</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_particles_html_a09aa053be160e695627643c64d111d96"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a09aa053be160e695627643c64d111d96">SPH::DiffusionReactionParticles::diffusion_dt_</a></div><div class="ttdeci">StdVec&lt; StdLargeVec&lt; Real &gt; &gt; diffusion_dt_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:53</div></div>
<div class="ttc" id="abase__body_8h_html"><div class="ttname"><a href="base__body_8h.html">base_body.h</a></div><div class="ttdoc">This is the base classes of SPH bodies. The real body is for that with cell linked list and the ficti...</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_s_p_h_body_html"><div class="ttname"><a href="class_s_p_h_1_1_s_p_h_body.html">SPH::SPHBody</a></div><div class="ttdoc">SPHBody is a base body with basic data and functions. Its derived class can be a real fluid body,...</div><div class="ttdef"><b>Definition:</b> base_body.h:63</div></div>
<div class="ttc" id="anamespace_s_p_h_html"><div class="ttname"><a href="namespace_s_p_h.html">SPH</a></div><div class="ttdef"><b>Definition:</b> solid_body_supplementary.cpp:9</div></div>
<div class="ttc" id="aclass_s_p_h_1_1_diffusion_reaction_particles_html_a8bf449802715f840b83c056a140dd2e4"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_particles.html#a8bf449802715f840b83c056a140dd2e4">SPH::DiffusionReactionParticles::number_of_diffusion_species_</a></div><div class="ttdeci">size_t number_of_diffusion_species_</div><div class="ttdef"><b>Definition:</b> diffusion_reaction_particles.h:49</div></div>
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